YAML header

Global options for outputs/formatting

Markdown

Plain text formatting allows for conversion to multiple document types

Chunks

# This is a chunk of R code that adds an image
knitr::include_graphics("images/example_chunk.png")

Output types

• PDF: requires \(\LaTeX\) to compile (see TinyTeX distribution)
• HTML
• Microsoft Office (Word/Powerpoint)

YAML specification

• Use output argument in YAML header
• Pay attention to indentation and colons
• Press knit button or command/CTRL-shift-K

Render

• Render file in console: rmarkdown::render(file, output_format)
• Option to create PDF from HTML: pagedown::chrome_print(file)

Built-in templates

• Presentations
  • ioslides and Slidy for HTML
  • Beamer for PDF
• Shiny documents and presentations (interactive)

R packages

• Presentations: revealjs
• CVs: vitae
• Academic posters: posterdown
• APA articles: papaja
• Journal templates: rticles

User-defined templates

\(\LaTeX\) templates

User-defined templates

Word Document

YAML parameters

• General YAML parameters
• Template-specific parameters (look at package documentation)

YAML references

These files go in the same place as your .Rmd

• Bibliography: .bib (I use BibDesk for my reference manager)
• Bibiography style: .csl (see my CV and Psychonomics poster repos for APA 6 files)
• \(\LaTeX\) styling: .cls
• HTML styling: .css
• Interacting with pandoc: .lua (multiple bibliographies)

Inline \(\LaTeX\)  and CSS code

• \(\LaTeX\) with PDFs
  • Calling \(\LaTeX\) packages
  • Using symbols: here and here
  • Using type-setting commands (e.g., \vspace{12pt})
• CSS with HTML

\(\LaTeX\)

Examples from my stats homework

\(\LaTeX\)

CSS/HTML

Examples from my Psychonomics poster

Editing template documents

# Make dataframe with installed packages
pkgs <- installed.packages() %>%
  as.data.frame()

# Pull posterdown package 
pstr <- pkgs %>% 
  select(Package, LibPath, Version, Depends, Imports) %>%
  dplyr::filter(Package == "posterdown")

# Make table
kable(pstr) %>%
  kable_styling(bootstrap_options = "condensed", 
                font_size = 18)

Editing template documents

• Save the original template and move it to a different location
• Make one change at a time
• Name the updated template with the same name in the same place as the original

Identifying issues

• Warnings vs. errors
• Console vs. chunk
• Markdown environment vs. R environment
• Package specification :: for unloaded packages and conflicts

Warnings

Warnings won’t stop your document from compiling, but generally indicate that you should change something in your code

Errors

Chunk error

Markdown/YAML error

R code and environments

Running a chunk executes the code in the console and adds the output to your R environment

R code and environments

Your R environment is separate from the environment created by “knitting” a document

y <- 100
# print(x + y) works when I run this chunk, but fails when knitting
print(y)

## [1] 100

Tips

• Clear all variables: rm(ls = list())
• Restart R environment: control/CTRL + fn + shift + F10
• Run all chunks individually in order before compiling to test code
• Google package and error

Stack Overflow is your friend!

Random tidbits

• Escape characters with a backslash \
• Call R objects in Markdown by ~sandwiching~ with backticks ``
• Automatic bracket/quote/asterisk wrapping
• Dollar signs for \(\LaTeX\) math mode (but also be careful with pandoc)
• Line spacing matters in markup

Other packages/tools

• Sublime Text text editor
• scholar package for automatically downloading citations from Google Scholar
• devtools package for installing packages/plug-ins from GitHub (e.g., papaja)
• wordcountaddin plug-in for checking word count and readability

Updating software/packages

• Update your TeX distribution from the command line
• Update all packages (including rmarkdown) in library with update.packages(path)
• Update individual packages by reinstalling with install.packages(package)
• Update R in the console with updateR package
• Redownload RStudio to update